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- PDB-9etu: Archaellum filament from the Halobacterium salinarum deltaAgl27 strain -

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Basic information

Entry
Database: PDB / ID: 9etu
TitleArchaellum filament from the Halobacterium salinarum deltaAgl27 strain
ComponentsArchaellin
KeywordsSTRUCTURAL PROTEIN / archaellum / haloarcheon / archaellin
Biological speciesHalobacterium salinarum (Halophile)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsGrossman-Haham, I. / Shahar, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Perturbed N-glycosylation of Halobacterium salinarum archaellum filaments leads to filament bundling and compromised cell motility
Authors: Mashni, L. / Vershinin, Z. / Zalk, R. / Shahar, A. / Eichler, J. / Grossman-Haham, I.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaellin
B: Archaellin
C: Archaellin
D: Archaellin
E: Archaellin
F: Archaellin
G: Archaellin
H: Archaellin
I: Archaellin
J: Archaellin
K: Archaellin
L: Archaellin
M: Archaellin
N: Archaellin
O: Archaellin
P: Archaellin
Q: Archaellin
R: Archaellin
S: Archaellin
T: Archaellin
U: Archaellin
V: Archaellin
W: Archaellin
X: Archaellin
Y: Archaellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,32375
Polymers502,69925
Non-polymers30,62350
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Archaellin


Mass: 20107.971 Da / Num. of mol.: 25 / Source method: isolated from a natural source
Details: Since Hbt. salinarum encodes five archaellins (i.e., FlaA1, FlaA2, FlaB1, FlaB2, and FlaB3) and their arrangement within the archaellum filaments is unknown, we further refined the cryo-EM ...Details: Since Hbt. salinarum encodes five archaellins (i.e., FlaA1, FlaA2, FlaB1, FlaB2, and FlaB3) and their arrangement within the archaellum filaments is unknown, we further refined the cryo-EM map without applying symmetry, in an attempt to resolve the positions of these archaellins within the filament, as done previously with reconstruction of the Methanocaldococcus villosus archaellum. Symmetry-free refinement improved the overall resolution map to 3.1 A and revealed differences in density among archaellin subunits. Nonetheless, we were unable to identify features that would allow us to unambiguously assign specific archaellins into the density, perhaps because the regions that distinguish each archaellin are few, short, and mostly predicted to lack defined secondary structure, or because the five archaellins are not organized in a repeating pattern. Consequently, we built a model into the central region of the cryo-EM map comprising 26 archaellin subunits that share a consensus sequence, in which identical residues among the five archaellins are explicitly modelled, with those variable residues usually being modelled as alanine residues (UNK).
Source: (natural) Halobacterium salinarum (Halophile)
#2: Polysaccharide...
3-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-beta-D-glucopyranuronic acid-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 612.468 Da / Num. of mol.: 50 / Source method: obtained synthetically
DescriptorTypeProgram
[]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-GlcpA]{[(4+1)][a-L-IdopA3SO3]{}}}}LINUCSPDB-CARE
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Archaellum filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.020466 MDa / Experimental value: NO
Source (natural)Organism: Halobacterium salinarum (Halophile)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_4985: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 107.91 ° / Axial rise/subunit: 5.46 Å / Axial symmetry: C1
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265906 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00234090
ELECTRON MICROSCOPYf_angle_d0.66146921
ELECTRON MICROSCOPYf_dihedral_angle_d7.5926728
ELECTRON MICROSCOPYf_chiral_restr0.046428
ELECTRON MICROSCOPYf_plane_restr0.0035553

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